Ontology highlight
ABSTRACT:
PROVIDER: PRJNA473434 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7229580.fastq.gz | Fastqsanger.gz | |||
| SRR7229581.fastq.gz | Fastqsanger.gz | |||
| SRR7229582.fastq.gz | Fastqsanger.gz | |||
| SRR7229583.fastq.gz | Fastqsanger.gz | |||
| SRR7229575.fastq.gz | Fastqsanger.gz |
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Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO
Project description:To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
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Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:Accurate description of a microbial community is an important first step in understanding the role of its components in ecosystem function. A method for surveying microbial communities termed Serial Analysis of Ribosomal DNA (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA gene from microbial communities. These tags are ligated to form concatemers comprised of 20-40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method’s utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. Comparison of duplicate profiles from one soil genomic DNA preparation revealed the method was highly reproducible. The large numbers of singleton tags together with non-parametric richness estimates indicated a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either numerical or diversity standpoints, low abundant taxa comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological role of these rare members of microbial communities in qualitative and quantitative terms. Keywords: SARD profiles, culture-independent study, microbial community survey, microbial census
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Project description:Desert microbial communities live in a pulsed ecosystem shaped by isolated and rare precipitation events. The Namib desert is one of the oldest continuously hyperarid ecosystems on Earth. In this study, surface microbial communities of open soils (without sheltering features like rocks, vegetation or biological soil crusts) are analysed. We designed an artificial rainfall experiment where a 7x7 (3.5 x 3.5 m) plot remained dry while an adjacent one received a 30 mm simulated rain. Samples were taken randomly in parallel from both plots at 10 min, 1 h, 3 h, 7 h, 24 h and 7 days after the watering moment. Duplicate libraries were generated from total (rRNA depleted) RNA and sequenced 2x150 bp in an Illumina Hiseq 4000 instrument.
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Project description:Global warming substantially changes precipitation patterns in the Tibetan plateau, with projection of increased precipitation in southern and northern Tibet but decreased precipitation in the center. Understanding mechanisms of such changes in greenhouse gas emissions is of vital importance in predicting ecosystem feedbacks to climate changes. Nonetheless, it has been hampered by limited knowledge in soil microbial communities, one of the major drivers of greenhouse gas emission. Here, we report a field experiment simulating drying and wetting conditions in the Tibetan grassland. Our field site is located at the Haibei Alpine Grassland Ecosystem Research Station in the northeast of Tibet Plateau, China, and we employed GeoChip 5.0 180K to analyze microbial responses. 18 samples were collected from 3 plots in Haibei Station, with 6 replicates in each plot
2016-05-28 | E-GEOD-82006 | biostudies-arrayexpress
Project description:Global warming substantially changes precipitation patterns in the Tibetan plateau, with projection of increased precipitation in southern and northern Tibet but decreased precipitation in the center. Understanding mechanisms of such changes in greenhouse gas emissions is of vital importance in predicting ecosystem feedbacks to climate changes. Nonetheless, it has been hampered by limited knowledge in soil microbial communities, one of the major drivers of greenhouse gas emission. Here, we report a field experiment simulating drying and wetting conditions in the Tibetan grassland. Our field site is located at the Haibei Alpine Grassland Ecosystem Research Station in the northeast of Tibet Plateau, China, and we employed GeoChip 5.0 180K to analyze microbial responses.
2016-05-28 | GSE82006 | GEO
Project description:Herein, we evaluated the changes in biological functions in soils across global biomes through the identification and quantification of proteins. This knowledge is essential to provide one stepforward in soil microbial ecology in order to decipher the cellular and molecular mechanisms employed by soil microbial communities to adapt to their environment and to explain the potential responses of microbial communities, and their microbially-driven ecosystem services, to global change and land use. Our study aims to provide the most comprehensive assessment on the structure and function of the topsoil metaproteome across global biomes, and hence provide direct identification of the most domimant protein-encoded functions in terrestrial ecosystems.
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Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
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Project description:The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.
2016-02-22 | GSE77866 | GEO